There are a few theories which are supported by the in-game sources, Vix details them in his Details of the Dwemer, Part 3. My theory is that they were moved to some outer realm or maybe moved in time, like Alduin. If that's the case they can certainly return at any time
You'd get more of your share of answers if you put this on the lore discussion. A lot of loremasters there.
Anyway, he's right. There are a couple of in-game books about the Dunmer that tells of the circumstances leading to disappearance of the dwemer (some in mythical proportions, according to some in-game book, some have some grain of truth in it.). Read some in-game books about the Dunmer. They are the race most associated with the Dwemer (in terms of contact; the Dunmer have been in war with them ever since they were still the Chimer).
The question of whether or not they will return is a matter of speculation, as there is not even a hint about that in the lore. So, I leave that to your opinion.